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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:LMCD1-PBX3

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LMCD1-PBX3
	FusionPDB ID: 45770
	FusionGDB2.0 ID: 45770
		Hgene	Tgene
	Gene symbol	LMCD1	PBX3
	Gene ID	29995	5090
	Gene name	LIM and cysteine rich domains 1	PBX homeobox 3
	Synonyms	-	-
	Cytomap	3p25.3	9q33.3
	Type of gene	protein-coding	protein-coding
	Description	LIM and cysteine-rich domains protein 1dyxin	pre-B-cell leukemia transcription factor 3homeobox protein PBX3pre-B-cell leukemia homeobox 3
	Modification date	20200313	20200320
	UniProtAcc	Q9NZU5	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000157600, ENST00000535732, ENST00000397386, ENST00000454244,	ENST00000538998, ENST00000373483, ENST00000447726, ENST00000342287, ENST00000373487, ENST00000373489,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 2 X 2=8	10 X 10 X 7=700
	# samples	2	12
	** MAII score	log2(2/8*10)=1.32192809488736	log2(12/700*10)=-2.54432051622381 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: LMCD1 [Title/Abstract] AND PBX3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LMCD1(8543667)-PBX3(128691932), # samples:2
Anticipated loss of major functional domain due to fusion event.	LMCD1-PBX3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. LMCD1-PBX3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. LMCD1-PBX3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. LMCD1-PBX3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Fusion gene breakpoints across LMCD1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across PBX3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChiTaRS5.0	N/A	DA020849	LMCD1	chr3	8543667	+	PBX3	chr9	128691932	+
ChiTaRS5.0	N/A	DA020867	LMCD1	chr3	8543667	+	PBX3	chr9	128691932	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000157600	LMCD1	chr3	8543667	+	ENST00000342287	PBX3	chr9	128691932	+	2404	274	13	813	266
ENST00000157600	LMCD1	chr3	8543667	+	ENST00000373487	PBX3	chr9	128691932	+	2580	274	13	1125	370
ENST00000157600	LMCD1	chr3	8543667	+	ENST00000373489	PBX3	chr9	128691932	+	2244	274	13	1062	349
ENST00000535732	LMCD1	chr3	8543667	+	ENST00000342287	PBX3	chr9	128691932	+	2286	156	27	695	222
ENST00000535732	LMCD1	chr3	8543667	+	ENST00000373487	PBX3	chr9	128691932	+	2462	156	27	1007	326
ENST00000535732	LMCD1	chr3	8543667	+	ENST00000373489	PBX3	chr9	128691932	+	2126	156	27	944	305

DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000157600	ENST00000342287	LMCD1	chr3	8543667	+	PBX3	chr9	128691932	+	0.002447649	0.99755234
ENST00000157600	ENST00000373487	LMCD1	chr3	8543667	+	PBX3	chr9	128691932	+	0.000614634	0.99938536
ENST00000157600	ENST00000373489	LMCD1	chr3	8543667	+	PBX3	chr9	128691932	+	0.001359245	0.9986407
ENST00000535732	ENST00000342287	LMCD1	chr3	8543667	+	PBX3	chr9	128691932	+	0.003313019	0.996687
ENST00000535732	ENST00000373487	LMCD1	chr3	8543667	+	PBX3	chr9	128691932	+	0.000500394	0.99949956
ENST00000535732	ENST00000373489	LMCD1	chr3	8543667	+	PBX3	chr9	128691932	+	0.001095184	0.9989048

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>45770_45770_1_LMCD1-PBX3_LMCD1_chr3_8543667_ENST00000157600_PBX3_chr9_128691932_ENST00000342287_length(amino acids)=266AA_BP=87
MGLAGLARAPARSGWRGFRGSPALQLKRPSCAWLRTELPPRPANLAIQPPLSPLRALAPLPEKPGAVPPPQKRMAKVAKDLNPGVKKACN
EFTTHVMNLLREQSRTRPISPKEIERMVGIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSE

--------------------------------------------------------------

>45770_45770_2_LMCD1-PBX3_LMCD1_chr3_8543667_ENST00000157600_PBX3_chr9_128691932_ENST00000373487_length(amino acids)=370AA_BP=87
MGLAGLARAPARSGWRGFRGSPALQLKRPSCAWLRTELPPRPANLAIQPPLSPLRALAPLPEKPGAVPPPQKRMAKVAKDLNPGVKKACN
EFTTHVMNLLREQSRTRPISPKEIERMVGIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSE
EAKEELAKKCSITVSQSLVKDPKERGSKGSDIQPTSVVSNWFGNKRIRYKKNIGKFQEEANLYAAKTAVTAAHAVAAAVQNNQTNSPTTP
NSGSSGSFNLPNSGDMFMNMQSLNGDSYQGSQVGANVQSQVDTLRHVINQTGGYSDGLGGNSLYSPHNLNANGGWQDATTPSSVTSPTEG

--------------------------------------------------------------

>45770_45770_3_LMCD1-PBX3_LMCD1_chr3_8543667_ENST00000157600_PBX3_chr9_128691932_ENST00000373489_length(amino acids)=349AA_BP=87
MGLAGLARAPARSGWRGFRGSPALQLKRPSCAWLRTELPPRPANLAIQPPLSPLRALAPLPEKPGAVPPPQKRMAKVAKDLNPGVKKACN
EFTTHVMNLLREQSRTRPISPKEIERMVGIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSE
EAKEELAKKCSITVSQVSNWFGNKRIRYKKNIGKFQEEANLYAAKTAVTAAHAVAAAVQNNQTNSPTTPNSGSSGSFNLPNSGDMFMNMQ

--------------------------------------------------------------

>45770_45770_4_LMCD1-PBX3_LMCD1_chr3_8543667_ENST00000535732_PBX3_chr9_128691932_ENST00000342287_length(amino acids)=222AA_BP=43
MAIQPPLSPLRALAPLPEKPGAVPPPQKRMAKVAKDLNPGVKKACNEFTTHVMNLLREQSRTRPISPKEIERMVGIIHRKFSSIQMQLKQ
STCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKKCSITVSQVSNWFGNKRIRYKKNIGKFQEEANLYAA

--------------------------------------------------------------

>45770_45770_5_LMCD1-PBX3_LMCD1_chr3_8543667_ENST00000535732_PBX3_chr9_128691932_ENST00000373487_length(amino acids)=326AA_BP=43
MAIQPPLSPLRALAPLPEKPGAVPPPQKRMAKVAKDLNPGVKKACNEFTTHVMNLLREQSRTRPISPKEIERMVGIIHRKFSSIQMQLKQ
STCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKKCSITVSQSLVKDPKERGSKGSDIQPTSVVSNWFGN
KRIRYKKNIGKFQEEANLYAAKTAVTAAHAVAAAVQNNQTNSPTTPNSGSSGSFNLPNSGDMFMNMQSLNGDSYQGSQVGANVQSQVDTL

--------------------------------------------------------------

>45770_45770_6_LMCD1-PBX3_LMCD1_chr3_8543667_ENST00000535732_PBX3_chr9_128691932_ENST00000373489_length(amino acids)=305AA_BP=43
MAIQPPLSPLRALAPLPEKPGAVPPPQKRMAKVAKDLNPGVKKACNEFTTHVMNLLREQSRTRPISPKEIERMVGIIHRKFSSIQMQLKQ
STCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKKCSITVSQVSNWFGNKRIRYKKNIGKFQEEANLYAA
KTAVTAAHAVAAAVQNNQTNSPTTPNSGSSGSFNLPNSGDMFMNMQSLNGDSYQGSQVGANVQSQVDTLRHVINQTGGYSDGLGGNSLYS

--------------------------------------------------------------

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:8543667/chr9:128691932)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
LMCD1 Q9NZU5	.
FUNCTION: Transcriptional cofactor that restricts GATA6 function by inhibiting DNA-binding, resulting in repression of GATA6 transcriptional activation of downstream target genes. Represses GATA6-mediated trans activation of lung- and cardiac tissue-specific promoters. Inhibits DNA-binding by GATA4 and GATA1 to the cTNC promoter (By similarity). Plays a critical role in the development of cardiac hypertrophy via activation of calcineurin/nuclear factor of activated T-cells signaling pathway. {ECO:0000250, ECO:0000269\|PubMed:20026769}.	FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000373483

130_138

254.0

Compositional bias

Note=Poly-Ala

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000447726

130_138

97.0

360.0

Compositional bias

Note=Poly-Ala

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000342287

235_297

172.0

764.6666666666666

DNA binding

Homeobox%3B TALE-type

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000373483

235_297

254.0

DNA binding

Homeobox%3B TALE-type

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000373489

235_297

172.0

435.0

DNA binding

Homeobox%3B TALE-type

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000447726

235_297

97.0

360.0

DNA binding

Homeobox%3B TALE-type

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000373483

43_234

254.0

Domain

PBC

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

LMCD1

chr3:8543667

chr9:128691932

ENST00000157600

28_58

14.0

366.0

Compositional bias

Note=Cys-rich

Hgene

LMCD1

chr3:8543667

chr9:128691932

ENST00000157600

241_306

14.0

366.0

Domain

LIM zinc-binding 1

Hgene

LMCD1

chr3:8543667

chr9:128691932

ENST00000157600

307_365

14.0

366.0

Domain

LIM zinc-binding 2

Hgene

LMCD1

chr3:8543667

chr9:128691932

ENST00000157600

99_206

14.0

366.0

Domain

PET

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000342287

130_138

172.0

764.6666666666666

Compositional bias

Note=Poly-Ala

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000373489

130_138

172.0

435.0

Compositional bias

Note=Poly-Ala

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000342287

43_234

172.0

764.6666666666666

Domain

PBC

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000373489

43_234

172.0

435.0

Domain

PBC

Tgene

PBX3

chr3:8543667

chr9:128691932

ENST00000447726

43_234

97.0

360.0

Domain

PBC

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>730_LMCD1_8543667_PBX3_128691932_ranked_0.pdb	LMCD1	8543667	8543667	ENST00000373489	PBX3	chr9	128691932	+	MGLAGLARAPARSGWRGFRGSPALQLKRPSCAWLRTELPPRPANLAIQPPLSPLRALAPLPEKPGAVPPPQKRMAKVAKDLNPGVKKACN EFTTHVMNLLREQSRTRPISPKEIERMVGIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSE EAKEELAKKCSITVSQSLVKDPKERGSKGSDIQPTSVVSNWFGNKRIRYKKNIGKFQEEANLYAAKTAVTAAHAVAAAVQNNQTNSPTTP NSGSSGSFNLPNSGDMFMNMQSLNGDSYQGSQVGANVQSQVDTLRHVINQTGGYSDGLGGNSLYSPHNLNANGGWQDATTPSSVTSPTEG	370

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

LMCD1_pLDDT.png

PBX3_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
LMCD1
PBX3

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to LMCD1-PBX3

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to LMCD1-PBX3

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source